*The cell surface streptavidin project approaches targeting from a different direction, that is, from the cell. While the adaptamer project uses nucleic acids to target any two substrates to each other, the cell surface streptavidin project seeks to target any substrate(s) to the cell surface.

+

*The method of targeting would be implemented through the '''expression of streptavidin protein on the cell surface'''. Streptavidin is a protein which binds strongly to the biotin molecule, thus there is a common practice of biotinylating (adding biotin to) nucleic acids or peptides for streptavidin affinity purification or antibody conjugation. We would be utilizing this strong streptavidin-biotin binding to target <u>any</u> biotinylated nucleic acid or peptide to the outside of a cell expressing streptavidin on the surface. Here are some potentially useful applications.

+

**bringing a biotinylated protein to the cell surface for facilitated interaction with some other surface element.

+

**linking a cell with another protein/cell via a biotinylated aptamer.

+

**delivering a DNA nanobox to the cell surface through a biotinylated oligonucleotide.

-

'''Scaffold 1: GPI anchor'''

+

*Streptavidin would be expressed on the cell surface through the '''Lpp-OmpA surface display vehicle''' (Earhart, 2000). The complete vehicle consists of three fused protein domains.

+

**Signal peptide of lipoprotein (Lpp). This targets the protein to the outer membrane.

+

** Transmembrane domains of outer membrane protein A (OmpA). This spans the protein across the outer membrane to the cell surface.

+

**The surface protein.

-

'''Scaffold 2: Beta autotransporter'''

+

*Assembly of the fusion protein would be carried out through a '''modified BioBricks assembly for protein domains''' (Phillips and Silver, 2006). Standard BioBricks parts separated from the flanking XbaI and SpeI sites by a single spacer nucleotide, in order to prevent Dam methylation. If you leave out these spacer nucleotides, the mixed site formed between assembled parts is six base pairs long, and so reading frame can be maintained between assembled protein domains.

#Where can we get the DNA expressing the scaffold protein. I need to look more into this, but I don't think we can just order it.

+

*We completed assembly of constructs using the following BioBrick parts.

-

#Where do we get streptavidin DNA (smaller problem)

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**J04500. a composite part of a lac promoter (R0010) and a strong ribosome binding site (B0031)

-

#What constraints do we have to worry about with streptavidin? In the original and later autotransporter papers, the passenger protein was mutated to lack cysteines in order to prevent disulfide bond formation in the periplasm: tertiary structure prevents passage of the protein through the beta barrel.

+

**J36835. Lpp, the lipoprotein signal peptide.

-

#How much time to get a first experiment up and running? This depends on how much work we have to do with the scaffold protein sequence and how fast we can get them (likely a long time).

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**J36837 or J36838. OmpA, one (O1) or five (O5) transmembrane domains, respectively. Both have been shown to work (Earhart, 2000).

-

#Will we be able to correspond with experts on this system? The founder of autodisplay, Joachim Jose, has not responded to some intial questions about autotransporter.

***Note: Streptavidin exists naturally as a soluble tetramer, but restriction to the surface might allow only monomeric/dimeric forms. What is interesting is that there has been research done to engineer such forms, in order to render biotin binding less strong but more easily reversible (Wu, 2005).

+

*Western blots were performed with transformed and induced cells, probing with anti-his6 antibody (each streptavidin had a His6 tag) and with anti-streptavidin antibody. Distinct bands were observed at the expected sizes in anti-his6 probing, and bands were observed at the same places with the anti-streptavidin probing. These results suggest the following.

+

**The promoter and ribosome binding site are functioning correctly for expression of these fusion protein construct.

+

**The BioBricks assembly of the fusion protein was successful in that reading frame was maintained, since the coding sequence for the His6 tag is found at the end of the construct.

+

**The streptavidin part of the fusion protein is still folding in such a way that anti-streptavidin antibody can recognize it.

-

==Demonstrate control of a nucleic acid interface between proteins and the cell surface==

(Maybe Un-, but more likely..) fortunately, another group has done work like this. We'll expand on the "adaptamer" concept of Tahiri-Alaoui et al. (12000850). In this paper, the group evolved one aptamer which bound streptavidin, then spliced it to a CopA RNA. Then they spliced a complementary CopT RNA to a CD4 aptamer. Following CopA/CopT binding, the resulting construct could bind both CD4 and streptavidin. Neato. CopA and CopT bind each other by a kissing complex between two loops; mutations have been introduced before, so looking at those studies might be a good starting places for adjusting the dissociation rate (16199086).

+

=Future Plans=

-

+

*Now that we know that the construct is being expressed, we need to determine whether or not the construct is being localized to the outer membrane. We can separate the cell lysate by centrifugation, isolate the outer membrane proteins, and then perform Western blots, probing with anti-his6 and anti-streptavidin antibody.

-

The reason they go through the trouble of using CopA and CopT is that they maintain stable secondary structures; the group reports that when you just have any old complementary strands, the binding affinities of the aptamers goes down considerably. We may be able to design our own RNA-RNA interfaces to have well-defined secondary structure, enhancing our ability to control dissociation rate.

+

*If the construct is indeed being localized to the outer membrane, we then need to determine if the streptavidin is being displayed functionally on the cell surface. We can probe whole cells with anti-streptavidin antibodies or even fluorescently tagged streptavidin aptamers for in-cell westerns, or we can visualize surface binding of biotinylated, fluorescently tagged oligonucleotides under a microscope.

-

+

*If streptavidin is being expressed on the cell surface, we can switch in other engineered streptavidin clones and compare biotin binding. We can also try adding a length of amino acids between OmpA and streptavidin, which might give spatial flexibility to allow formation of tetramers on the cell surface or to allow the streptavidin to extend outside of any extracellular complexes.

-

Additionally, we want to make one of these aptamers bind to the E. coli cell surface. There is a serious dearth of known aptamers that do this. The only report about one is 15541352; their aptamer binds LPS, a major component of the E. coli outer membrane, so it has a lot of targets. They don't give a Kd value, maybe because it didn't matter too much with so much LPS. Hope we can get our hands on the sequence..

+

-

+

-

One thing to consider: in the absence of aptamers that bind to the cell surface, we might as well try it with aptamers that bind proteins in vitro as done in 12000850. Why worry about cells for now? We're interested in a proof of principle.

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-

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'''Initial experiment'''

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We'll attempt to build an adaptamer that can bind thrombin and streptavidin simultaneously. More details to come. Oligos to be used [[/thrombstrepadapt/|here]]

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-

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<u>Major Questions/concerns</u>

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-

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#What aptamers exist that bind the E. coli cell surface??? (and have public sequences! The sequence of the aptamer that binds LPS is not reported in the paper.)

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#Is there any chance that we'll be able to evolve our own aptamer this summer? Online resources point toward 'no' but see last question.

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#What other secondary structures might work as interfaces? If we design our own, the online programs mfold and Vienna RNA may be useful. Otherwise, we'll have to go with known complementary structures. Do the faculty members have any suggestions for structures?

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#Time and reliability: Hopefully short! Aptamer sequences are relatively short, so we'll likely be able to order them instead of asking groups for them. Then we'd try tons of intermediate interfaces, which is just a matter of ordering more oligos.

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#Will people respond to email? I've emailed David Liu about evolving aptamers and Sulatha Dwarakanath (author of 15541352) about aptamers that target the E. coli cell surface to no response. It would be quite helpful to hear their thoughts.

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-

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==Other projects==

+

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A couple of related projects that we haven't really researched..

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#Having E. coli export an aptamer outside the cell

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#Using aptamers to actually stimulate a response on the cell surface

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-

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=Experiments, Updates=

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==Streptavidin Fusion Protein==

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===6/30===

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I have contacted Filiz Aslan at DFCI, and she has agreed to give me clones of her single-chain dimeric streptavidin (Aslan et al., 2005). I'm in the process of having the MTA (Material Transfer Agreement) approved by Harvard's Office of Technology Development. Once the approval has gone through, we can pick up the clone!

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-

+

-

I've also gotten a reply from Dr. Takeshi Sano, also at DFCI. He has pTSA13-wt, which is wild-type streptavidin clone. Another MTA will have to be approved.

+

-

+

-

I have word from Dr. Charles Earhart that his colleague Dr. George Georgiou "has been distributing LppOmpA vector plasmids and has a large collection." I've emailed Dr. Georgiou several times without reply. I tried emailing his administrative assistant Donna, and she replied she would pass it along to someone in the lab. Closer? Maybe.

+

-

+

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We may be able to make Dr. Georgiou's construct ourselves. It is a fusion protein N - Lpp aa's 1-9 - OmpA aa's 46-159 - surface protein - C. E. coli K12 genome and BioBrick primers for the full OmpA gene (start through stop) have been ordered.

+

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[[User:Perry|Perry]] 14:45, 30 June 2006 (EDT)

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===7/3===

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I got a reply from Mark Howarth (Howarth et al, 2006) from the Ting Lab at MIT. He kindly offered to give me three clones of streptavidin: wild-type, wild-type + His6 tag, non-biotin-binding mutant (N23A, S27D, S45A), in pET21a plasmid; I went to MIT and picked them up.

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-

+

-

[[User:Perry|Perry]] 13:25, 3 July 2006 (EDT)

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===7/7===

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GPI anchors and autotransporter are almost dead. No group ever got back to us about supplying plasmids. The autotransporter vector was derived from an enteropathic E. coli (strain 2787 [O126:H27]). Genomic DNA of another enteropathic E. coli, O157:H7 str. Sakai, is available for purchase. However, the AIDA-I gene differs considerably between these two strains, so it may not be worth attempting to PCR out.

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-

+

-

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==Adaptamers==

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===7/7===

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Adaptamers:

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-

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-

We've received the short DNA sequences that we'll be using. We are waiting for purified streptavidin protein to come in. The main question is what we will use in our gel shift assay. We cannot use 32P, so our alternatives are:

The first kit uses fluorescent dyes. We would need to buy a $600 filter for the gel imager to use it. The second two involve blotting membranes. Since this project will probably involve trying out a few types of aptamer sequences and many types of intermediate sequences between the two aptamer ends, the latter two, while supposedly more reliable, will likely be too costly. Licor also has a system based on fluorescent dyes but it looks like you buy the parts separately...

+

-

+

-

Alain suggested that all adaptamers that we create have a sequence that can bind a complementary short sequence; we'd order a lot of labeled short complementary sequence. Sounds like a good idea, as long as those short sequences do not interfere with the aptamer binding.

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-

+

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===7/11===

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-

+

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Shawn and William suggested that for an initial assay, it'd be easy to just stain protein with Coomassie blue. So that's what we attempted.

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-

+

-

We ran two 10-20% native polyacrylamide gels at 15 V overnight; the first used some lanes from the Nano group's gel. Visualization to come tomorrow.

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-

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-

The composition of what we added to each line is below; materials were added and incubated for 30 minutes in 2 uL total volume for lanes 1-11, 1-12 prior to dilution to 10 uL including addition of loading dye. Lanes 2-1 to 2-9 were incubated for an hour; longer incubation carried out since DNA basepairing reactions for lanes 2-10 to 2-12 were carried out for 30 minutes using results from 30-minute incubations of lanes 2-1 to 2-9. This incubation time should not be significant.

The gels came out completely blank. Bummer. Potential problems were protein concentration, pH of reaction buffer, and voltage. Different concentrations were tried out by the nanogroup to no success.

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=Reading=

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-

+

-

A suggestion: although it might be bad form, when citing an article, just refer to the PMID. This is more useful than the pretty pubmed link which isn't smart enough to know when you are logged in with a HUID.

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+

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==General Fusion==

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<biblio>

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#fusion1 pmid=1367360

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#fusion2 pmid=2476847

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#fusion3 pmid=2548185

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#fusion4 pmid=3079747

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#fusion5 pmid=7691170

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#fusion6 pmid=15695809

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</biblio>

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==E. coli cell surface display==

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<biblio>

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#display1 pmid=16369779

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#display2 pmid=11024362

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#display3 pmid=9624691

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-

#display4 pmid=12039531

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#display5 pmid=

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</biblio>

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'''Notes on Autodisplay review (display1) 16369779'''

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This is a review about the Autodisplay system used to express proteins on the E. coli cell surface. Some of the important features of this system are:

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*Utilizes E.coli-native AIDA-I as scaffold

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*Detection: monoclonal antibodies and protease cleavage sites created

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*Protein unfolded during transport to cell surface.

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*Variety of proteins have been displayed (p.610)

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*Possibly to display catalytically active enzymes.

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*Dimerization of proteins has been observed! (unique to this system); work on tetramers in progress. Protein anchor floats around membrane.

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*Many proteins displayed: ~10^5 without loss of cell viability

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The writer claims that the system is superior compared to all other display systems, but he might be biased since he created it.

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'''Notes on expressing genes in different compartments review (display2) 11024362'''

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This is a more general review which is actually mostly about cell-surface display techniques. It offers a wider range of options, but came out in 2000, so new options probably have become available.

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*5 options; a good summary is found on page 3.

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**Porins- Insert protein <= 60 residues

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**Fimbriae- Insert protein <= 15 residues

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**Lipoproteins

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**GPI anchor

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**Beta-autotransporter - same system as that used in display1

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*The latter three were claimed to support large polypeptides. However, looking at a few of the articles seemed to suggest that they actually only tried them out with small polypeptides. The winners appear to be GPI anchors and beta autotransporters, although this might have changed in recent years. See display3 for the use of GPI anchors.

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'''GPI anchor(display3) 9624691'''

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Functional levansucrase bound to a GPI anchor, Inp, was expressed on the E. coli cell surface. Using these cells, they successfully converted sucrose to levan. Levansucrase, is about 400 a.a. residues long.

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'''More bacterial display (display4) 12039531'''

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This review's gram-negative bacteria section is slightly more recent than display1 but contains almost no more information. It does have more explicit weight constraints on the proteins you can display for each system and pays slightly more attention to other constraints, but nothing that interesting. It has an equally comprehensive section on gram-positive bacteria. You might as well look at this one and not display1, though because it was published in 2002 vs. 2000 for display1.

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It does mention that gram-positive bacteria are more suitable for display. Tested gram-postive display systems are better at displaying large proteins. Additionally, protein only need pass through one membrane versus moving through the cytoplasmic membrane and achieving the correct orientation in the outer membrane. Finally, gram-positive bacteria are more durable and easier to test under harsh lab procedures.

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==Aptamers and Adaptamers==

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<biblio>

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#apt1 pmid=15541352

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#apt2 pmid=11808691

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#apt3 pmid=12000850

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#apt4 pmid=16199086

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#apt5 pmid=10744017

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#apt6 pmid=1741036

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#apt7 pmid=12219078

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</biblio>

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<br>

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'''Quantum dots conjugated to aptamers (apt1) 15541352'''

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This was a neat study in which quantum dots were conjugated to antibodies or aptamers that target E. coli cell surfaces. The point of the article is that the emissions from the quantum dots changed following binding, but what's relevant to us is the aptamer they used. They evolved it on their own using the method of apt2 (probably out of convenience: both were Austin-based companies). The aptamer recognizes lipopolysaccharide (LPS O111:B4). I am currently emailing to find out why they chose LPS. At least we know of one aptamer that binds the E. coli cell surface...

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'''Adaptamers (apt3) 12000850'''

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This paper is also listed in the streptavidin section. See "Notes" under "Demonstrate Control.." project for a description.

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'''CopA/CopT (apt4) 16199086'''

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This recent review paper has a description of the CopA/CopT interaction which is utilized in apt3.

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'''CopA/CopT (apt5) 10744017'''

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This paper reveals the extremely intricate "deep-kissing" structure formed between CopA and CopT.

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'''Thrombin (apt6) 1741036'''

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Paper talking about selection for a DNA aptamer that binds thrombin. Seems like no one's evolved a better version yet: even recent papers talk about the same motif (16616893).

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'''DNA aptamer to streptavidin (apt7)'''

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David Liu's paper about selecting for a DNA aptamer that binds streptavidin. The point here was using the nonhomolous random recombination instead of error-prone PCR to select for aptamers. The point for us is that it gives a DNA aptamer that binds streptavidin pretty well (40 bp motif kD ~100 nM).

As the title sugggests, a group was actually able to express _tetrameric_ streptavidin on the B. subtilis cell surface. This was a lot easier than doing it in other types of bacteria since they didn't have to worry about getting across the cell membrane or cell wall: when B. subtilis forms spores, a bunch of proteins form in the cytosol which then become the coats of spores... Additionally, spores form approximately when cells stop dividing, which somehow defeats the biotin sequestration problem. Actually, they never do a specific experiment to show this, but we are probably supposed to infer that it was enough to just see the streptavidin on the surface(?) Regardless, this organism is pretty different from E. coli, so it probably isn't terribly important.

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==ompA==

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<biblio>

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#ompA1 pmid=16391137

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#ompA2 pmid=9005446

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#ompA3 pmid=8920186

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#ompA4 pmid=6313361

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#ompA5 pmid=1557377

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#ompA6 pmid=12209821

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#ompA7 pmid=11036660

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</biblio>

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==Related articles==

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<biblio>

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#other1 pmid=9893944

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</biblio>

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<br>

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'''Cd2+ binding (other1) 9893944'''

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other1 is an old review article I came across talking about expressing metallothioneins on the cell surface of E. coli; these things bind Cd2+, so those interested in pollution cleanup might want to take a look.

Current revision

Project Overview

The cell surface streptavidin project approaches targeting from a different direction, that is, from the cell. While the adaptamer project uses nucleic acids to target any two substrates to each other, the cell surface streptavidin project seeks to target any substrate(s) to the cell surface.

The method of targeting would be implemented through the expression of streptavidin protein on the cell surface. Streptavidin is a protein which binds strongly to the biotin molecule, thus there is a common practice of biotinylating (adding biotin to) nucleic acids or peptides for streptavidin affinity purification or antibody conjugation. We would be utilizing this strong streptavidin-biotin binding to target any biotinylated nucleic acid or peptide to the outside of a cell expressing streptavidin on the surface. Here are some potentially useful applications.

bringing a biotinylated protein to the cell surface for facilitated interaction with some other surface element.

linking a cell with another protein/cell via a biotinylated aptamer.

delivering a DNA nanobox to the cell surface through a biotinylated oligonucleotide.

Streptavidin would be expressed on the cell surface through the Lpp-OmpA surface display vehicle (Earhart, 2000). The complete vehicle consists of three fused protein domains.

Signal peptide of lipoprotein (Lpp). This targets the protein to the outer membrane.

Transmembrane domains of outer membrane protein A (OmpA). This spans the protein across the outer membrane to the cell surface.

The surface protein.

Assembly of the fusion protein would be carried out through a modified BioBricks assembly for protein domains (Phillips and Silver, 2006). Standard BioBricks parts separated from the flanking XbaI and SpeI sites by a single spacer nucleotide, in order to prevent Dam methylation. If you leave out these spacer nucleotides, the mixed site formed between assembled parts is six base pairs long, and so reading frame can be maintained between assembled protein domains.

Lpp-OmpA surface display vehicle (Francisco et al., 1993)

Modified BioBricks assembly for protein domains

Results

We completed assembly of constructs using the following BioBrick parts.

J04500. a composite part of a lac promoter (R0010) and a strong ribosome binding site (B0031)

J36835. Lpp, the lipoprotein signal peptide.

J36837 or J36838. OmpA, one (O1) or five (O5) transmembrane domains, respectively. Both have been shown to work (Earhart, 2000).

Note: Streptavidin exists naturally as a soluble tetramer, but restriction to the surface might allow only monomeric/dimeric forms. What is interesting is that there has been research done to engineer such forms, in order to render biotin binding less strong but more easily reversible (Wu, 2005).

Western blots were performed with transformed and induced cells, probing with anti-his6 antibody (each streptavidin had a His6 tag) and with anti-streptavidin antibody. Distinct bands were observed at the expected sizes in anti-his6 probing, and bands were observed at the same places with the anti-streptavidin probing. These results suggest the following.

The promoter and ribosome binding site are functioning correctly for expression of these fusion protein construct.

The BioBricks assembly of the fusion protein was successful in that reading frame was maintained, since the coding sequence for the His6 tag is found at the end of the construct.

The streptavidin part of the fusion protein is still folding in such a way that anti-streptavidin antibody can recognize it.

Diagram of cell surface streptavidin construct

Western blots of cell surface streptavidin constructs

Future Plans

Now that we know that the construct is being expressed, we need to determine whether or not the construct is being localized to the outer membrane. We can separate the cell lysate by centrifugation, isolate the outer membrane proteins, and then perform Western blots, probing with anti-his6 and anti-streptavidin antibody.

If the construct is indeed being localized to the outer membrane, we then need to determine if the streptavidin is being displayed functionally on the cell surface. We can probe whole cells with anti-streptavidin antibodies or even fluorescently tagged streptavidin aptamers for in-cell westerns, or we can visualize surface binding of biotinylated, fluorescently tagged oligonucleotides under a microscope.

If streptavidin is being expressed on the cell surface, we can switch in other engineered streptavidin clones and compare biotin binding. We can also try adding a length of amino acids between OmpA and streptavidin, which might give spatial flexibility to allow formation of tetramers on the cell surface or to allow the streptavidin to extend outside of any extracellular complexes.